Millennial clonal persistence and transposable element-biased somatic mutations in an herbaceous plant (Typha latifolia)

clone_jzg22This script we used for jzg population analysis with 2022 refenrence data 01 build the reference genomeScripts we used for build the reference are in 01_ref. 02 check clone Scripts we used for checking clone and call variants are in 02_check_clone. 03 estimate population ageScripts we uesd for estimating the T. latifolia clonal population age in 03_estimate_population_age. 04 clonal development routesScripts we uesd for build the clonal phylogenetic tree, and map the tree to the geographic locations in 04_clonal_development_routes. 05 characteristic of somatic mutationsScripts we uesd for checking position, direction of somatic mutations. meanwhile, check the non-synonymous mutation site during the development and the vaf of somatic mutations in 05_position_direction_vaf. 06 data Files that we used as material or the file lists we used for analysis are in data.